tbuckley/cabot-search huggingface dataset:
Abstract 3117: Molecular and clinical correlates of genetic ancestry in a diverse, admixed cancer dataset
Authors: Mackenzie D. Postel, Jamie K. Teer, Steven A. Eschrich, Julie Dutil, Erin M. Siegel, William D. Cress, John D. Carpten, David W. Craig
Journal: Cancer Research (2023)

Abstract The objective of this study is to determine whether genetic ancestry analysis can provide additional insight into the genetic determinants of cancer disparities distinct from socially constructed variables like self-reported race and ethnicity. The Oncology Research Information Exchange Network (ORIEN) “Avatar” project is a diverse dataset of extensive, longitudinal clinical and molecular data from 18 cancer centers across the U.S.; the ORIEN Intermember Ancestry Project cohort described in this study is a subset of the larger dataset. Using paired tumor/germline whole exome sequencing data from ORIEN, the Genome Aggregation Database (gnomAD) dataset of ancestry reference individuals, and the software tools ADMIXTURE and RFMix, we have estimated genetic ancestry for cancer cases from both ORIEN and The Cancer Genome Atlas (TCGA). The ORIEN dataset has 2.6X greater representation of self-reported Hispanic/Latinos than does TCGA, with Hispanic/Latinos making up 9% of the ORIEN dataset vs. 4% in TCGA. As expected, individuals of Hispanic/Latino ethnicity are heterogeneous in their admixture proportions of Indigenous American, African, and European ancestries. We performed statistical analyses in R to identify molecular and clinical correlations with ancestry. This study highlights the clinical utility of genetic ancestry analysis as an approach to understand the genetic contributions to cancer disparities in diverse, admixed populations. Citation Format: Mackenzie D. Postel, Jamie K. Teer, Steven A. Eschrich, Julie Dutil, Erin M. Siegel, William D. Cress, John D. Carpten, David W. Craig. Molecular and clinical correlates of genetic ancestry in a diverse, admixed cancer dataset [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3117.
Abstract 1474: Hippo-mediated control of the mutant <i>TERT</i> promoter via MYC and GABP
Authors: Nicholas O. Stevers, Andrew Mancini, Joseph F. Costello
Journal: Cancer Research (2023)

Abstract Most cancers achieve replicative immortality through reactivation of telomerase reverse transcriptase (TERT), the rate limiting subunit in telomerase activity. Tumors from more than 50 distinct cancer types reactivate TERT expression via mutations in the TERT promoter. Understanding how the mutations lead to activation and immortality is a central question in cancer research. Oncogenic signaling pathways including EGFR/AMPK, MAPK, and C-MYC/ASL, have been linked to telomere maintenance via their regulation of the mutant TERT promoter. Two mutually exclusive point mutations in the TERT promoter generate a de novo E26 Transformation Specific (ETS) binding motif that recruits the GA-Binding Protein (GABP) multimeric complex to reactivate TERT expression (Bell et al, Science 2015). Recruitment of GABP to the mutant TERT promoter facilitates the recruitment of C-MYC to the promoter (Shi et al, Mol. Cell 2022), which aids in transcriptional activation. The Hippo pathway plays a key role in development, organ size determination, and homeostasis, and has been found dysregulated in numerous cancer types. GABP is a member of the Hippo pathway, with GABP activating the promoter of the Hippo transcriptional effector Yes-associated protein (YAP1) and the Hippo pathway core kinases stimulating GABP nuclear exit (Wu et al., Cell Reports 2013). We have found that YAP and its paralogue transcriptional coactivator with PDZ-binding motif (TAZ) are linked to mutant TERT promoter activation in glioblastoma via transcriptional activation of both GABPA and MYC. These observations suggest the Hippo pathway supports tumor immortality in glioblastoma. While immortality has proven to be an elusive target, further investigations of the signaling networks that converge on the activation of the mutant TERT promoter may reveal therapeutic targets that block tumor growth and have secondary benefit by their impact on tumor immortality. Citation Format: Nicholas O. Stevers, Andrew Mancini, Joseph F. Costello. Hippo-mediated control of the mutant TERT promoter via MYC and GABP [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1474.
Abstract 4458: Single cell landscape of multicentric Castleman disease in identical twins
Authors: Jason Yongsheng Chan, Jui Wan Loh, Jing Quan Lim, Herty Liany, Elizabeth Chun Yong Lee, Jing Yi Lee, Bavani Kannan, Boon Yee Lim, Kerry Lim, Jeslin Chian Hung Ha, Cedric Chuan-Young Ng, Tun Kiat Ko, Dachuan Huang, Dominique Yuan Bin Seow, Chee Leong Cheng, Sock Hoai Chan, Joanne Ngeow, Bin Tean Teh, Soon Thye Lim, Choon Kiat Ong
Journal: Cancer Research (2023)

Abstract Idiopathic Multicentric Castleman Disease (iMCD) is a rare IL-6-driven hematological disorder characterized by systemic lymphadenopathy, elevated immunoglobulin levels, and prominent plasmacytosis in the bone marrow and lymph nodes. An unusual occurrence of iMCD in identical twins provided a unique opportunity to answer genetic and molecular features of this disease, including the cell-of-origin of IL-6 signals, and the immune milieu within affected lymphoid organs and in circulation. Germline whole genome sequencing of the affected twins identified pathogenic homozygous mutations of NCOA4 c.G1322A and monoallelic mutations of TRAF3 c.G1504A - both genes recently implicated in IL-6 signaling and B-cell regulation. Their unaffected sister was heterozygous mutant for NCOA4 and homozygous wildtype for TRAF3 loci. Via single cell sequencing of 63,519 cells from bone marrow, lymph node, and peripheral blood mononuclear cells, we identified nodal endothelial cells and fibroblastic reticular cells (FRC) as the source of IL-6 signals. The latter are composed of mainly T-cell zone FRCs (CCL19+/CCL21+/IL7+/PDPN+/MADCAM1-) and a minor population of follicular dendritic cells (FDCs) (CD21+/CD35+/CXCL13+). An “inflammatory” peripheral monocytosis enriched for the expression of S100A family genes was evident in both twins, as well as a group of monocytes expressing cytotoxic gene signatures in the affected twin with milder clinical manifestations. Their unaffected sister mainly carried monocytes enriched for expression of major histocompatibility complex (MHC) class II genes. In conclusion, we provided evidence of a genetic cause of iMCD, identified the putative cell-of-origin of IL-6 signals in this rare disease, and described a distinct monocytic immune response phenotype. Citation Format: Jason Yongsheng Chan, Jui Wan Loh, Jing Quan Lim, Herty Liany, Elizabeth Chun Yong Lee, Jing Yi Lee, Bavani Kannan, Boon Yee Lim, Kerry Lim, Jeslin Chian Hung Ha, Cedric Chuan-Young Ng, Tun Kiat Ko, Dachuan Huang, Dominique Yuan Bin Seow, Chee Leong Cheng, Sock Hoai Chan, Joanne Ngeow, Bin Tean Teh, Soon Thye Lim, Choon Kiat Ong. Single cell landscape of multicentric Castleman disease in identical twins. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4458.
Abstract 3802: miR-199a and miR-199b stimulate the progression of diffuse gastric cancer through direct targeting of Frizzled-6
Authors: Jihye Park, Sieun Lee, Soon Auck Hong, Yoon Ho Ko, Young-Ho Ahn
Journal: Cancer Research (2023)

Abstract There is no pathological difference between early and advanced diffuse gastric cancer (DGC), particularly in the gastric mucosa. In this study, we tried to identify microRNAs (miRNAs) as diagnostic biomarkers that can differentiate between early and advanced DGC. miRNA expression profiling was performed by NanoString nCounter method in human DGC tumors. miR-199a and miR-199b (miR-199a/b) were particularly up-regulated in advanced DGC compared with early DGC. Ectopic expression of miR-199a/b accelerated growth, viability, and motility of SNU601, human GC cells, and expedited tumor development in a mouse xenograft model. miR-199a/b also inhibited cell adhesion. Through 3’-UTR luciferase assay, Frizzled-6 (FZD6) was confirmed as a direct target of miR-199a/b. siRNA-mediated depletion of FZD6 increased cell growth and motility and addback of FZD6 restored cell growth, motility, and adhesion. To explore their clinicopathological roles in patients, miR-199a/b levels were measured by in situ hybridization in human DGC tumor sections. High miR-199a/b was correlated with advanced lymphovascular invasion, advanced T stages, and lymph node metastasis. Collectively, miR-199a/b promote the progression of DGC via targeting FZD6. These results imply that miR-199a/b can be used as diagnostic and prognostic biomarkers of DGC. Citation Format: Jihye Park, Sieun Lee, Soon Auck Hong, Yoon Ho Ko, Young-Ho Ahn. miR-199a and miR-199b stimulate the progression of diffuse gastric cancer through direct targeting of Frizzled-6. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3802.
Abstract 6302: Identification of OASEP1 as a biomarker and therapeutic target for oral cancer
Authors: Atsushi Takano, Yoshihiro Yoshitake, Masahiro Shinohara, Yataro Daigo
Journal: Cancer Research (2023)

Abstract This study aims to identify new biomarkers and therapeutic targets for oral cancer. Our strategies are as follows: i) Identification of overexpressed genes in oral cancers by gene expression array analysis, ii) Validation of clinicopathologic significance of their protein expression by tissue microarray, iii) Examination of their growth effect on cancer cell by siRNAs. We identified a secreted protein, OASEP1 (oral cancer-associated serum protein 1) as a candidate. Immunohistochemical staining showed that OASEP1 protein expression was observed in 120 (75.4%) of 159 oral cancers that had undergone curative surgery. High level of OASEP1 expression was associated with poor prognosis for oral cancer patients (P = 0.0054, by log-rank test). Multivariate analysis revealed that strong OASEP1 expression was an independent prognostic factor. Suppression of OASEP1 expression by siRNA significantly inhibited the growth of oral cancer cell lines through apoptosis as detected by apoptosis assays and time lapse imaging. Transient OASEP1 overexpression significantly enhanced the growth of oral cancer cells. In addition, knock down of OASEP1 receptor by siRNAs also significantly inhibited the growth of oral cancer cells. Addition of OASEP1 protein significantly increased the growth of oral cancer cells in a dose dependent manner, suggesting that the interaction between OASEP1 and its receptor regulated the growth of oral cancer cells. Microarray analysis coupled with siRNAs for OASEP1 demonstrated various OASEP1-related oncogenic pathways in oral cancer cells. Our data suggest that OASEP1 is a possible prognostic biomarker and therapeutic target for oral cancer. Citation Format: Atsushi Takano, Yoshihiro Yoshitake, Masahiro Shinohara, Yataro Daigo. Identification of OASEP1 as a biomarker and therapeutic target for oral cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6302.
Abstract 5564: SerpinE2: A potential biomarker for urological cancers
Authors: Ruusu-Maaria Kovanen, Netta Koskinen, Timo-Pekka Lehto, Antti Rannikko, Tuomas Mirtti, Hannu Koistinen
Journal: Cancer Research (2023)

Abstract SerpinE2, also known as protease nexin-1, is an extracellular serine protease inhibitor modulating the activity of serine proteases such as thrombin, plasmin, urokinase-type plasminogen activator and trypsin. Dysregulation between extracellular serine proteases and their cognate inhibitors has been implicated in malignant progression, making serpins promising biomarkers for tumor progression and prognosis. SerpinE2 is upregulated in many cancers and promotes tumor invasion and metastasis. In this study, we analyzed serpinE2 expression by immunohistochemistry on tissue microarrays comprising of samples from prostate, bladder and kidney cancers. The studied samples were clinically hard-to-risk stratify and thus relevant for biomarker studies. We aimed to study the association of serpinE2 expression with survival and clinicopathological features in all three cancers, and evaluate its potential as an immunohistochemical biomarker. In the case of bladder cancer, association of serpinE2 expression with response to neoadjuvant chemotherapy was also assessed. We found that although the strong expression of serpinE2 was related to more aggressive prostate cancers (p = 0.017) and high grade bladder cancers (p = 0.034), it was not associated with relapse, treatment response or survival of prostate and bladder cancer patients. In renal cancer, on the contrary, serpinE2 expression was significantly lower in patients with tumor relapse (p = 0.048) and high expression predicted favorable disease-specific survival (p = 0.013). Our findings help understanding the functional role of serpinE2 in cancer progression and guide the prognostic biomarker research of serpinE2, particularly for prediction of renal cancer-specific survival. Citation Format: Ruusu-Maaria Kovanen, Netta Koskinen, Timo-Pekka Lehto, Antti Rannikko, Tuomas Mirtti, Hannu Koistinen. SerpinE2: A potential biomarker for urological cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5564.
Abstract 6352: Combination treatment with recombinant murine IL-12 and anti-PD-1 antibody enhanced anti-tumor efficacy through the activation of cytotoxic T cell response
Authors: Yeng-Jey Yang, Pei-Yi Tsou, Shiuh-Dih Chou, Meng-Na Lee, San-Chi Chen
Journal: Cancer Research (2023)

Abstract Introduction: Immune checkpoint inhibitors (ICIs) are widely used in cancer therapy. Among them, anti-PD-1 antibodies are the most used and have been approved by FDA for the treatment of many types of cancer (1). In our previous studies, combination of anti-PD-1 antibody with IL-12 demonstrated significant synergistic effect on tumor growth inhibition. The elevation of IFN-γ mRNA expression suggested the potential roles of CD8 T cells and NK cells in this process. In this study, we used two syngeneic mice tumor models to investigate the mechanisms of synergistic effect by the combination of IL-12 and anti-PD-1 antibody. Methods: We used syngeneic mice tumor models with mice cancer cell lines CT-26 and MC-38. The mice inoculated with tumor cells and were treated until tumors grew to 100 mm3. The mice were divided into three groups to receive the treatment, including rmIL-12 alone, anti-PD1-antibody alone, and the combination of rmIL-12 and anti-PD1-antibody (BIW x 3 weeks). At the end of the study, the mice were sacrificed and tumor resection and splenectomy were performed. The tumor infiltrating lymphocyte subpopulations within the tumor microenvironment were analyzed by flow cytometry and gene expression profile by RNA Seq. Results: The combination of rmIL-12 and anti-PD-1 antibody significantly inhibited tumor growth compared to the treatment with rmIL-12 and anti-PD-1 antibody alone. The combination group demonstrated more CD8+ T cell in the tumor microenvironment via flow cytometry. In addition, RNA Seq showed the combination group increased CD8+ T cells, NK cells, and Th1 populations. The levels of cytotoxicity related genes (IFN-γ, Granzyme B, Perforin) were also higher in combination group. Conclusion: Combination of rmIL-12 and anti-PD-1 antibody increased immune cells infiltration in the tumor microenvironment and enhanced anti-tumor response suggesting the potential of this combination for cancer treatment. Citation:(1). Watson, G.A. et al. (2020) “Novel strategies in immune checkpoint inhibitor drug development: How far are we from the paradigm shift?,” British Journal of Clinical Pharmacology, 86(9), pp. 1753-1768. https://doi.org/10.1111/bcp.14355. Citation Format: Yeng-Jey Yang, Pei-Yi Tsou, Shiuh-Dih Chou, Meng-Na Lee, San-Chi Chen. Combination treatment with recombinant murine IL-12 and anti-PD-1 antibody enhanced anti-tumor efficacy through the activation of cytotoxic T cell response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6352.
Abstract 6328: An off-the-shelf Twin BiTE combination therapy controls heterogenous glioblastoma and shapes immune response
Authors: Filippo Rossignoli, Paulo Borges, Rebecca Lumia, Khalid Shah
Journal: Cancer Research (2023)

Abstract Glioblastoma (GBM) is the most common primary brain tumor in adults, characterized by a median survival of 12-14 months with less than 10% of patients surviving at least 2 years from diagnosis. The discovery of tumor-associated antigens (TAAs) has permitted development of a new array of therapeutic strategies that selectively target GBM and spare normal cells of the CNS. In this study we used an alternative off-the-shelf approach to activate the immune system and direct it against the tumor, taking into account antigen heterogeneity and TME immune suppression without the need of engineering the patient’s immune cells. We generated TAA-targeting Bispecific T-cell Engagers (BiTEs) and engineered adult stem cells to secrete twin BiTEs (T-BiTE-SC). The approach was tested in combination with in naïve T cells on established and primary patient-derived cell lines expressing various levels of the target antigens. Moreover, to further support the therapeutic action of T cells, and combat immune-suppressive microenvironment and exhaustion, we combined our T-BiTE SC with an immune-stimulating cytokine. We show the efficacy of the individual BiTEs against different primary and established tumor cell lines. Moreover, the T-BiTE-SC, significantly controlled the growth of a tumor expressing heterogeneous levels of the targeted antigens. The immune stimulation reduced T cell exhaustion and consolidated a Th1 phenotype. Altogether our study demonstrated the feasibility and efficacy of an off-the-shelf immunotherapy, based on BiTEs simultaneously targeting tumor heterogeneity without the need for direct engineering of the immune cells. Citation Format: Filippo Rossignoli, Paulo Borges, Rebecca Lumia, Khalid Shah. An off-the-shelf Twin BiTE combination therapy controls heterogenous glioblastoma and shapes immune response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6328.
Abstract 186: <i>Cellos</i>: High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology
Authors: Patience Mukashyaka, Pooja Kumar, Dave Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Olga Anczukow, Edison T. Liu, Jeffrey H. Chuang
Journal: Cancer Research (2023)

Abstract Three-dimensional (3D) culture models, such as organoids, are flexible systems to interrogate cellular growth, multicellular spatial architecture, and morphology in response to drug treatment, including the potential to resolve the individual behaviors and interactions of mixed cancer cell populations. However, new computational methods to segment and analyze 3D models at cellular resolution are needed to realize these possibilities. Here we report Cellos (Cell Organoid Segmentation), an accurate, high throughput image analysis pipeline for 3D organoid and nuclear segmentation analysis. Cellos segments 3D organoids using classical algorithms and segments nuclei using a Stardist-3D convolutional neural network trained on a manually annotated dataset of 3,862 cells from 36 organoids confocally imaged at 5 μm z-resolution. To evaluate the capabilities of Cellos, we then analyzed 74,450 organoids with 1.65 million cells from multiple experiments on triple negative breast cancer organoids containing clonal mixtures with complex cisplatin sensitivity. Cellos was able to accurately distinguish cell ratios in organoids in 96-well plates to within 2.99% and was effective for fluorescently labelled nuclei and independent DAPI stained datasets. Cellos was able to recapitulate traditional luminescence based drug responses by analyzing 3D images, including parallel analysis of multiple cancer clones in the same well. Moreover, Cellos was able to identify organoid and nuclear morphology feature changes associated with treatment. Finally, Cellos enables 3D analysis of cell spatial relationships, which we used to detect ecological affinity between cancer cells, beyond expectations from local cell division or organoid composition. Cellos provides powerful tools to perform high throughput analysis for pharmacological testing and biological investigation of organoids based on 3D imaging. Citation Format: Patience Mukashyaka, Pooja Kumar, Dave Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Olga Anczukow, Edison T. Liu, Jeffrey H. Chuang. Cellos: High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 186.